Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016145.1 Corchorus capsularis cultivar CVL-1 contig16166, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43873
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--78 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
79 CCTCCTTGAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:8139 original size:19 final size:18
Alignment explanation
Indices: 8106--8141 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8096 TTGAAATAAT
8106 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
8124 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
8142 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:11233 original size:23 final size:26
Alignment explanation
Indices: 11206--11257 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
11196 GACTCTATTG
11206 TTTTTTT-A-TCATTATTATTATTAA
1 TTTTTTTGAGTCATTATTATTATTAA
*
11230 TTTTTTTGAGTGATTATTATTATTAA
1 TTTTTTTGAGTCATTATTATTATTAA
11256 TT
1 TT
11258 AACAATAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.28
25 1 0.04
26 17 0.68
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (26 bp):
TTTTTTTGAGTCATTATTATTATTAA
Found at i:11821 original size:6 final size:6
Alignment explanation
Indices: 11810--11851 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
11800 ATTCAATATC
11810 ATCTAT ATCTAT ATCTAT ATCTAT A-C--T ATCTAT ATACTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT-CTAT AT
11852 ATAAAAGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 1 0.03
6 22 0.69
7 6 0.19
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
ATCTAT
Found at i:11845 original size:11 final size:11
Alignment explanation
Indices: 11812--11854 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
11802 TCAATATCAT
*
11812 CTATATCTATA
1 CTATATATATA
*
11823 TCTATATCTATA
1 -CTATATATATA
*
11835 CTATCTATATA
1 CTATATATATA
11846 CTATATATA
1 CTATATATA
11855 AAAGTACGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (11 bp):
CTATATATATA
Found at i:11948 original size:31 final size:31
Alignment explanation
Indices: 11883--11943 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
11873 AACTTTATGT
* *
11883 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
11914 TTTCCAATTGTACCCTT-TTTTAAAAA-ATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
11943 T
1 T
11944 ATTTCTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 8 0.29
31 16 0.57
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTAAAAACATA
Found at i:12327 original size:19 final size:20
Alignment explanation
Indices: 12300--12337 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12290 TACTATTATT
12300 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
12320 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
12338 ACTATTATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:14821 original size:30 final size:29
Alignment explanation
Indices: 14753--14830 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
14743 AATTACCATG
* *
14753 ATTAACTTCATTCCCTAAACTCGTACACC
1 ATTAACTTCATTCACTAAACTCGTACAAC
* * *
14782 ATCAACTTCATTCTCTAAATTC-TCAGCAAC
1 ATTAACTTCATTCACTAAACTCGT-A-CAAC
14812 ATTAACTTCATTCACTAAA
1 ATTAACTTCATTCACTAAA
14831 ATTGTCAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.02
29 20 0.49
30 20 0.49
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
ATTAACTTCATTCACTAAACTCGTACAAC
Found at i:24917 original size:41 final size:41
Alignment explanation
Indices: 24860--24982 Score: 228
Period size: 41 Copynumber: 3.0 Consensus size: 41
24850 AACTTAGATG
24860 ATGCTGAATTATCTACATAATCCAAAGGGGTACGTGAAATA
1 ATGCTGAATTATCTACATAATCCAAAGGGGTACGTGAAATA
24901 ATGCTGAATTATCTACATAATCCAAAGGGGTACGTGAAATA
1 ATGCTGAATTATCTACATAATCCAAAGGGGTACGTGAAATA
*
24942 ATGCTGAATTATCTACATAATCCAGAGGGGTACGTGCAAAT
1 ATGCTGAATTATCTACATAATCCAAAGGGGTACGTG-AAAT
24983 CTAGCACACA
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
41 76 0.95
42 4 0.05
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (41 bp):
ATGCTGAATTATCTACATAATCCAAAGGGGTACGTGAAATA
Found at i:38710 original size:24 final size:25
Alignment explanation
Indices: 38650--38708 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
38640 TTCAAACCCT
*
38650 AAACTTCATTTCTAACAACCTCTTC
1 AAACTTCATTTCTAACAACATCTTC
38675 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
38699 AAA-TTCATTT
1 AAACTTCATTT
38709 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:38742 original size:11 final size:11
Alignment explanation
Indices: 38728--38776 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 11
38718 TTAATCATAA
38728 ACTAATTAAAT
1 ACTAATTAAAT
38739 ACTAATTAATCAT
1 ACTAATTAA--AT
*
38752 AAACTAATTAGAT
1 --ACTAATTAAAT
38765 ACTAATTAAAT
1 ACTAATTAAAT
38776 A
1 A
38777 TAAACTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 20 0.62
13 4 0.12
15 8 0.25
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:38747 original size:26 final size:26
Alignment explanation
Indices: 38718--38785 Score: 111
Period size: 26 Copynumber: 2.6 Consensus size: 26
38708 TTCCTTCATT
38718 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
38744 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
38770 TTAAAT-ATAAACTAAT
1 TT-AATCATAAACTAAT
38786 AAACAAAGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 37 0.93
27 3 0.08
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:38748 original size:15 final size:15
Alignment explanation
Indices: 38718--38761 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
38708 TTCCTTCATT
38718 TTAATCATAAACTAA
1 TTAATCATAAACTAA
38733 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
38744 TTAATCATAAACTAA
1 TTAATCATAAACTAA
38759 TTA
1 TTA
38762 GATACTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.36
13 4 0.16
15 12 0.48
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:38785 original size:15 final size:14
Alignment explanation
Indices: 38718--38785 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
38708 TTCCTTCATT
38718 TTAATCATAAACTAA
1 TTAAT-ATAAACTAA
38733 TTAA-AT--ACTAA
1 TTAATATAAACTAA
38744 TTAATCATAAACTAA
1 TTAAT-ATAAACTAA
*
38759 TT-AGAT--ACTAA
1 TTAATATAAACTAA
38770 TTAAATATAAACTAA
1 TT-AATATAAACTAA
38785 T
1 T
38786 AAACAAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
13 9 0.21
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.35
Consensus pattern (14 bp):
TTAATATAAACTAA
Found at i:39803 original size:2 final size:2
Alignment explanation
Indices: 39792--39828 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
39782 TTCAAGTTCC
39792 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39829 TACATGTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:42481 original size:429 final size:429
Alignment explanation
Indices: 41682--42522 Score: 1070
Period size: 429 Copynumber: 2.0 Consensus size: 429
41672 TTAAATCAAG
** *
41682 TAAGATAGAATTTGTAAAGGTTTAAGTAGTATAAAATAGAAAAGTATGAGGGTGATTTGATAACT
1 TAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAATAGAAAAGTATGAGGGTCATTTGATAACT
* * * *
41747 AATTCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAAATTTCCTTTTGAACCCTT
66 AATCCAAATAAGAAAATATTTGTTAATGAAGATCTTGAAACATAAAAATTCCCTTTTCAACCCTT
* * * * * * *
41812 CATGAAACTCATAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTTGTAGATTATACAGTAACC
131 AACGAAACTCATAGATCAAATTAACTTTCGGGTCCTTCATGAAAGTCGTAAATCATACAATAACC
* * * * * * ***
41877 TTTTTAACCGACATTTGAATAACTTTAATTGCACATGTGGATCGAAAATTATATGGTATTAAATA
196 TTTTTAACCGACACTTCAATAACTTCAATCGCACATGTGGATCAAAAACTATACAATATTAAATA
* * * * * * **
41942 GACCAACAATCGAAACGACCACATTTAGGAAGCATTTTTTTTGAATTGAAACATAAAAATTTGCT
261 GACCAACAACCAAAACCACAAAATTTAGGAAGCATTTTTTTAGAATCAAAACATAAAAATTTGCT
* * * *
42007 TTTGAATCCTTCATGAAAGATGTAGATTATGAAATTATCTTTTAATA-GACACATGAATCAAC-T
326 TTTGAATCCTTAATGAAAGATGTAGATCATAAAATTACCTTTTAATAGGA-ACATGAAT-AACTT
*
42070 TAATCGGACAAATAGAACAAAAAATAAAAAAATAAAGCGAT
389 TAATCGGACAAATAGAAAAAAAAATAAAAAAATAAAGCGAT
* *
42111 TAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTATAAAAGTATGAGGGTCATTTGATCAA-
1 TAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAATAGAAAAGTATGAGGGTCATTTGAT-AAC
42175 TAATCCAAATAAGAAAATATTTGTTAATGAAGATCTTGAAACATAAAAATTCCCTTTTCAACCCT
65 TAATCCAAATAAGAAAATATTTGTTAATGAAGATCTTGAAACATAAAAATTCCCTTTTCAACCCT
* * *
42240 TAACGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCATGGAAA-TCGTAAATCATGCAATA
130 TAACGAAACTCATAGATCAAA-TTAACTTTCGGGTCCTTCAT-GAAAGTCGTAAATCATACAATA
* *
42304 ACC-TTTTGACCGACACTTCAATAACTTCAATCGGACATGTGGA-CAAAAAACTATACAATATTA
193 ACCTTTTTAACCGACACTTCAATAACTTCAATCGCACATGTGGATC-AAAAACTATACAATATTA
** * * *
42367 AATTA-ACCGGCAACCAAAACCACAAAATTTCGGAAGCATTTTTTTAGAATCAAAATATTAAAA-
257 AA-TAGACCAACAACCAAAACCACAAAATTTAGGAAGCATTTTTTTAGAATCAAAACATAAAAAT
* * * *
42430 TTGACTTTTGAGTTCTTAATGAAA-ATTGTAGGTCATAAAATTACCTTTTAATAGGAACTTGAAT
321 TTG-CTTTTGAATCCTTAATGAAAGA-TGTAGATCATAAAATTACCTTTTAATAGGAACATGAAT
42494 AACTTTAATCGGACAAATAGAAAAAAAAA
384 AACTTTAATCGGACAAATAGAAAAAAAAA
42523 ACCAAAATAA
Statistics
Matches: 351, Mismatches: 52, Indels: 18
0.83 0.12 0.04
Matches are distributed among these distances:
428 8 0.02
429 300 0.85
430 39 0.11
431 4 0.01
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (429 bp):
TAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAATAGAAAAGTATGAGGGTCATTTGATAACT
AATCCAAATAAGAAAATATTTGTTAATGAAGATCTTGAAACATAAAAATTCCCTTTTCAACCCTT
AACGAAACTCATAGATCAAATTAACTTTCGGGTCCTTCATGAAAGTCGTAAATCATACAATAACC
TTTTTAACCGACACTTCAATAACTTCAATCGCACATGTGGATCAAAAACTATACAATATTAAATA
GACCAACAACCAAAACCACAAAATTTAGGAAGCATTTTTTTAGAATCAAAACATAAAAATTTGCT
TTTGAATCCTTAATGAAAGATGTAGATCATAAAATTACCTTTTAATAGGAACATGAATAACTTTA
ATCGGACAAATAGAAAAAAAAATAAAAAAATAAAGCGAT
Found at i:43142 original size:30 final size:30
Alignment explanation
Indices: 43108--43181 Score: 132
Period size: 29 Copynumber: 2.5 Consensus size: 30
43098 TTTGTTCTAG
*
43108 TATTAAAATGGTTTTTTTTTTGGCAATAGT
1 TATTAAAATTGTTTTTTTTTTGGCAATAGT
43138 TATTAAAATTG-TTTTTTTTTGGCAATAGT
1 TATTAAAATTGTTTTTTTTTTGGCAATAGT
43167 TATTAAAATTGTTTT
1 TATTAAAATTGTTTT
43182 ATTGCCTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 29 0.69
30 13 0.31
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
TATTAAAATTGTTTTTTTTTTGGCAATAGT
Done.